knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
library(tidyverse)
library(here)
library(broom)

# Time series packages
library(tsibble)
library(feasts)
library(lubridate)
library(fable)

Overview

An aerial view of Willamette Falls and the former Blue Heron paper mill. The Oregonian

Located about 10 miles south of Portland, Oregon on the Willamette River, Willamette Falls is the largest waterfall in the Northwestern United States. Despite a complicated industrial past, the falls have been a native salmon and lamprey fishery for thousands of years and see many more species of fish pass through since the first fish ladder was constructed in 1885. The Oregon Department of Fish and WIldlife maintains a fish counting station at Willamette Falls, allowing biologists to monitor populations over time.

Aerial View of Willamette Falls. 2010. Escapement Estimate of Adult Pacific Lamprey at Willamette Falls. by Baker, C., J. Graham, Confederate Tribes of the Warm Springs Reservation. Oregon Department of Fish and Wildlife. 2010. p. 4.

For this time series analysis we will use adult fish count data, recorded from 2001-01-01 to 2010-12-31. This data includes daily observations of 13 different fish species that pass through the Willamette Falls fish ladder. This data was shared by and accessed from Columbia River DART (Data Access in Real Time), part of the Colombia Basin Research project at University of Washington’s School of Aquatic & Fisheries Management.

Original time series

### read in fish count data
fish_df <- read_csv(here("data/willamette_fish_passage.csv")) %>% 
  janitor::clean_names() %>% 
  mutate(date = as.Date(date, format = "%m/%d/%y")) ###change date col from haracter to date class

fish_df[is.na(fish_df)] <- 0 ### replace NA's with 0 

fish_ts <- as_tsibble(fish_df, key = NULL, index = date) %>% ### change data frame to tsibble
  select(date, coho, jack_coho, steelhead) ### select date and species of interest

coho_plot <- ggplot(data = fish_ts,
       aes(x = date)) +
  geom_line(aes(y = coho),
            color = "darksalmon") +
  labs(x = " ",
       y = " ") +
  theme_minimal()

steel_plot <- ggplot(data = fish_ts,
       aes(x = date)) +
  geom_line(aes(y = steelhead),
            color = "darkseagreen") +
  labs(x = "",
       y = "") +
  theme_minimal()

jcoho_plot <- ggplot(data = fish_ts,
       aes(x = date)) +
  geom_line(aes(y = jack_coho),
            color = "azure3") +
  labs(x = "Date",
       y = "") +
  theme_minimal()


  

  
cowplot::plot_grid(coho_plot, steel_plot, jcoho_plot,
                   labels = c(" Coho    ", "Steelhead", "Jack Coho"), 
                   vjust=-0.5,
                   hjust = -0.2,
                   ncol = 1) +
  theme(plot.margin = unit(c(1, 0, 0, 0), "cm"))

Seasonplots

Annual counts by species